I found out what causes the NPCs to disappear after talking to you instead of correctly executing the EscapeArea command. It is caused by the map not being "properly" explored around the NPC. I used the Console to ExploreArea() and that prevents the issue from happening.

If Ascension64 was still around, I am sure it'd not take him long to remedy the situation but I have no idea how to fix this so I am hoping someone can come help.

So if they don't "know" where the exit is, they just "jump" at it. Interesting.

Yep, Jarno Mikkola. my Mega Mod FAQ. Use of the BWS, and how to use it(scroll down that post a bit).
OK, desert dweller, welcome to the sanity, you are free to search for the limit, it's out there, we drew it in the sand. Ouh, actually it was still snow then.. but anyways.

I found out what causes the NPCs to disappear after talking to you instead of correctly executing the EscapeArea command. It is caused by the map not being "properly" explored around the NPC. I used the Console to ExploreArea() and that prevents the issue from happening.

If Ascension64 was still around, I am sure it'd not take him long to remedy the situation but I have no idea how to fix this so I am hoping someone can come help.

Makes sense - and fits to the randomness and behaviour observed with the issue.

Well, I suppose there is little/no interest in this but I have worked on my own solution to the problem

In short, I went through the .d list and changed the EscapeAreaDestroy(90) to MoveToPointNoInterrupt([X,Y])DestroySelf() for the majority of the NPCs (some were unused, some were a bit too complex, some spawned in different areas and in some cases the file was shared).

It was a tedious process and typos are a concrete possibility. There has been only partial testing but if someone is interested, I am easy to reach.

If you want to, you should attach the source(before you made changes) and resulting files(after you made your fixes), as those can be diff-ed, and made into patch files that are then easy to apply in BWS.

Yep, Jarno Mikkola. my Mega Mod FAQ. Use of the BWS, and how to use it(scroll down that post a bit).
OK, desert dweller, welcome to the sanity, you are free to search for the limit, it's out there, we drew it in the sand. Ouh, actually it was still snow then.. but anyways.